Is it worth reading if we liked these notes? Does he elaborate much on specifics about these ideas? Or do these notes sum up everything fairly thoroughly?

[Systems with hysteresis cannot be made sense of with a timeless black-box analysis.]

Is this actually true, though? I'm inclined to think that your black-box analysis was badly done if it can't account for hysteresis. Time is only relevant to the system insofar as time describes the rate at which various parts of the system do things, which makes it seem like it's something that can be accounted for in indirect terms. Using indirect terms might be less efficient, but I don't see any reason to believe it's impossible.

I disagree that black box thinking is something we should strive to avoid. It seems too useful to me, and rather unavoidable anyways. Of course any particular black box model may be an oversimplification, but models that don't try to aim themselves at simplicity are going to fail due to Occam's Razor. (Also, in what sense is black box thinking a reductionist bias? It seems like the quintessential holistic bias to me.)